Back to Long Tests report for BioC 3.14

This page was generated on 2022-04-09 21:00:02 -0400 (Sat, 09 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4322
riesling1Windows Server 2019 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4108
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4135
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for cBioPortalData on nebbiolo2


To the developers/maintainers of the cBioPortalData package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 10/19HostnameOS / ArchCHECK
cBioPortalData 2.6.1  (landing page)
Marcel Ramos
Snapshot Date: 2022-04-09 06:55:01 -0400 (Sat, 09 Apr 2022)
git_url: https://git.bioconductor.org/packages/cBioPortalData
git_branch: RELEASE_3_14
git_last_commit: d97dfe4
git_last_commit_date: 2022-01-27 20:23:11 -0400 (Thu, 27 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  WARNINGS  
riesling1Windows Server 2019 Standard / x64  WARNINGS  
machv2macOS 10.14.6 Mojave / x86_64  WARNINGS  

Summary

Package: cBioPortalData
Version: 2.6.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no cBioPortalData_2.6.1.tar.gz
StartedAt: 2022-04-09 08:09:47 -0400 (Sat, 09 Apr 2022)
EndedAt: 2022-04-09 08:12:16 -0400 (Sat, 09 Apr 2022)
EllapsedTime: 148.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: cBioPortalData.Rcheck
Warnings: 3

Tests output


'R CMD check' output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no cBioPortalData_2.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc-longtests/meat/cBioPortalData.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘cBioPortalData/DESCRIPTION’ ... OK
* this is package ‘cBioPortalData’ version ‘2.6.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cBioPortalData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
Warning: 'studiesTable' is deprecated; see 'getStudies()'
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: 'studiesTable' is deprecated; see 'getStudies()'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... NOTE
Warning: 'studiesTable' is deprecated; see 'getStudies()'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
 WARNING
directory ‘longtests’ not found
* DONE

Status: 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc-longtests/meat/cBioPortalData.Rcheck/00check.log’
for details.



Installation output

cBioPortalData.Rcheck/00install.out

* installing *source* package ‘cBioPortalData’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cBioPortalData)